require(extrafont)
require(tidyverse)
library(ggpubr)
library(gridExtra)
library(cowplot)
cbPalette <- c( "#000000","#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")

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Data¶

##### load the node data frame for the bipartite graph
nodes <- read.csv("BipartiteNetwork_nodes.csv")
head(nodes)

Figure 3a¶

##### created in gephi and saved as png
gephi1<-ggdraw() +
   draw_image("Bipart.png")
gephi1

Figure 3b¶

tol_muted<- c('#332288','#44AA99','#117733','#999933','#DDCC77','#CC6677','#882255','#88CCEE')

phylo_bipaplotlegend <- ggplot(nodes)+
                geom_point(data=subset(nodes,Type=='TE'),aes(x=x,y=y),color="#d9d9d9",size=0.01)+
                geom_point(data=subset(nodes,Type=='Genome'),aes(x=x,y=y,color=Phylo),size=2,shape=19)+
                theme_void()+ theme(legend.position='bottom',legend.direction="vertical")+
                    scale_colour_manual(values=tol_muted)+scale_fill_manual(values=tol_muted)+
#                 scale_color_manual(values=pal8_no_light_yellow)+scale_fill_manual(values=pal8_no_light_yellow)+
                coord_fixed(ratio = 1)+labs(color='',fill='')+
                guides(color=guide_legend(,override.aes = list(size = 5,shape=15),ncol=4))+
    theme(text=element_text(size=15,  family="Times New Roman"))
phylo_bipaplotlegend

Figure 3c¶

bipa_piwiplot<- ggplot(nodes)+
    geom_point(data=subset(nodes,Type=='TE'),aes(x=x,y=y),colour="#d9d9d9",size=0.01)+
    geom_point(data=subset(nodes,Type=='Genome'),aes(x=x,y=y,color=PIWI),size=2)+
    theme_void()+#+scale_color_brewer(type='qual')+
    scale_color_manual(values=c('#31688EFF','#FDE725FF',"#d9d9d9" ),labels=c('no PIWI','PIWI','TEs'))+   
    labs(color='')+coord_fixed(ratio = 1)+
    guides(color=guide_legend(,override.aes=list(shape=15,size=5)))+
    theme(text=element_text(size=15,  family="Times New Roman"),legend.position='bottom')

bipa_piwiplot

Figure 3d¶

bipa_dnmtplot<- ggplot(nodes)+
    geom_point(data=subset(nodes,Type=='TE'),aes(x=x,y=y),colour="#d9d9d9",size=0.01)+
    geom_point(data=subset(nodes,Type=='Genome'),aes(x=x,y=y,color=DNMT),size=2)+
    theme_void()+ theme(legend.position='bottom')+
    scale_color_manual(values=c("#440154FF",'#35B779FF' ),labels=c('no DNMT','DNMT'))+
    labs(color='')+coord_fixed(ratio = 1)+
    guides(color=guide_legend(,override.aes=list(shape=15,size=5)))+
    theme(text=element_text(size=15,  family="Times New Roman"),legend.text.align = 0)
bipa_dnmtplot

Figure 3¶

options(repr.plot.width=15, repr.plot.height=15)


myfigure <- as_ggplot(arrangeGrob(gephi1,phylo_bipaplotlegend,bipa_piwiplot,bipa_dnmtplot, ncol=2,nrow=2))+                                
               draw_plot_label(label = c("A", "B", "C",'D'), size = 20,
                    x = c(0,0.5,0,0.5), 
                    y = c(1,1,0.5,0.5))
myfigure

Species	ID	Superfamily	piRNA	Weighted.Degree	Family	label_only_genomes	genome_size	Eigenvector.Centrality	g	⋯	y	x	Class	DNMT1	DNMT2	DNMT3	PIWI	DNMT	Phylo	Kuerzel
<fct>	<fct>	<fct>	<fct>	<int>	<fct>	<fct>	<fct>	<dbl>	<int>	⋯	<dbl>	<dbl>	<fct>	<fct>	<fct>	<fct>	<fct>	<fct>	<fct>	<fct>
Acanthocheilonema viteae	Acanthocheilonema_viteae	genome	0	1338727	genome	cheat	22034751.0	0.3059106	128	⋯	-213.04019	-323.57290	genome	-1	1	-1	-1	-1	Nematodes Clade III	A.vit
Acyrthosiphon pisum	Acyrthosiphon_pisum	genome	1	100734868	genome	cheat	541675271.0	0.5898820	209	⋯	-486.28683	-251.11584	genome	1	1	1	1	1	Arthropods	A.pis
Amphimedon queenslandica	Amphimedon_queenslandica	genome	0	43261462	genome	cheat	166678968.0	0.3290055	66	⋯	61.55285	-192.25584	genome	1	1	1	1	1	Other	A.que
Ancylostoma caninum	Ancylostoma_caninum	genome	1	81528305	genome	cheat	465749605.0	0.6383859	209	⋯	-854.83905	37.20678	genome	-1	1	-1	1	-1	Nematodes Clade V	A.can
Ancylostoma ceylanicum	Ancylostoma_ceylanicum	genome	1	66767534	genome	cheat	313092201.0	0.6013092	209	⋯	-936.88617	-24.83938	genome	-1	1	-1	1	-1	Nematodes Clade V	A.cey
Anopheles darlingi	Anopheles_darlingi	genome	1	2000107	genome	cheat	136949910.0	0.3382292	209	⋯	-11.72634	-108.50796	genome	-1	1	-1	1	-1	Arthropods	A.dar